niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__deblank_file_names.py

@@ -0,0 +1,210 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DEBLANK_FILE_NAMES_METADATA = Metadata(
+    id="da8da0abd18b50263679955b0ea74ae940b81571.boutiques",
+    name="@DeblankFileNames",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDeblankFileNamesParameters = typing.TypedDict('VDeblankFileNamesParameters', {
+    "__STYX_TYPE__": typing.Literal["@DeblankFileNames"],
+    "move": bool,
+    "nobrac": bool,
+    "demo_set": bool,
+    "echo": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@DeblankFileNames": v__deblank_file_names_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class VDeblankFileNamesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__deblank_file_names(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__deblank_file_names_params(
+    move: bool = False,
+    nobrac: bool = False,
+    demo_set: bool = False,
+    echo: bool = False,
+    help_: bool = False,
+) -> VDeblankFileNamesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        move: Actually rename the files (opposite of -dry_run).
+        nobrac: Do not replace () and [] in filenames, just spaces.
+        demo_set: Create a toy directory with bad names for testing.
+        echo: Turn on script echo.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@DeblankFileNames",
+        "move": move,
+        "nobrac": nobrac,
+        "demo_set": demo_set,
+        "echo": echo,
+        "help": help_,
+    }
+    return params
+
+
+def v__deblank_file_names_cargs(
+    params: VDeblankFileNamesParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("@DeblankFileNames")
+    if params.get("move"):
+        cargs.append("-move")
+    if params.get("nobrac"):
+        cargs.append("-nobrac")
+    if params.get("demo_set"):
+        cargs.append("-demo_set")
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("help"):
+        cargs.append("-help")
+    cargs.append("[FILES...]")
+    return cargs
+
+
+def v__deblank_file_names_outputs(
+    params: VDeblankFileNamesParameters,
+    execution: Execution,
+) -> VDeblankFileNamesOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = VDeblankFileNamesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__deblank_file_names_execute(
+    params: VDeblankFileNamesParameters,
+    execution: Execution,
+) -> VDeblankFileNamesOutputs:
+    """
+    A script to remove blanks and other annoying characters ([], ()) from filenames.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDeblankFileNamesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__deblank_file_names_cargs(params, execution)
+    ret = v__deblank_file_names_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__deblank_file_names(
+    move: bool = False,
+    nobrac: bool = False,
+    demo_set: bool = False,
+    echo: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VDeblankFileNamesOutputs:
+    """
+    A script to remove blanks and other annoying characters ([], ()) from filenames.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        move: Actually rename the files (opposite of -dry_run).
+        nobrac: Do not replace () and [] in filenames, just spaces.
+        demo_set: Create a toy directory with bad names for testing.
+        echo: Turn on script echo.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDeblankFileNamesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DEBLANK_FILE_NAMES_METADATA)
+    params = v__deblank_file_names_params(
+        move=move,
+        nobrac=nobrac,
+        demo_set=demo_set,
+        echo=echo,
+        help_=help_,
+    )
+    return v__deblank_file_names_execute(params, execution)
+
+
+__all__ = [
+    "VDeblankFileNamesOutputs",
+    "VDeblankFileNamesParameters",
+    "V__DEBLANK_FILE_NAMES_METADATA",
+    "v__deblank_file_names",
+    "v__deblank_file_names_params",
+]

niwrap_afni/afni/v__demo_prompt.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DEMO_PROMPT_METADATA = Metadata(
+    id="28759d07ed8faa73243bb8713758a156bb9ca999.boutiques",
+    name="@demo_prompt",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDemoPromptParameters = typing.TypedDict('VDemoPromptParameters', {
+    "__STYX_TYPE__": typing.Literal["@demo_prompt"],
+    "message": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@demo_prompt": v__demo_prompt_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "@demo_prompt": v__demo_prompt_outputs,
+    }.get(t)
+
+
+class VDemoPromptOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__demo_prompt(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    status: OutputPathType
+    """Status output: 0 if user presses OK, 1 if user cancels"""
+
+
+def v__demo_prompt_params(
+    message: str,
+) -> VDemoPromptParameters:
+    """
+    Build parameters.
+    
+    Args:
+        message: The message to display in the prompt.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@demo_prompt",
+        "message": message,
+    }
+    return params
+
+
+def v__demo_prompt_cargs(
+    params: VDemoPromptParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("@demo_prompt")
+    cargs.append(params.get("message"))
+    return cargs
+
+
+def v__demo_prompt_outputs(
+    params: VDemoPromptParameters,
+    execution: Execution,
+) -> VDemoPromptOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = VDemoPromptOutputs(
+        root=execution.output_file("."),
+        status=execution.output_file("status"),
+    )
+    return ret
+
+
+def v__demo_prompt_execute(
+    params: VDemoPromptParameters,
+    execution: Execution,
+) -> VDemoPromptOutputs:
+    """
+    Prompts user with a message and waits for acknowledgment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDemoPromptOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__demo_prompt_cargs(params, execution)
+    ret = v__demo_prompt_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__demo_prompt(
+    message: str,
+    runner: Runner | None = None,
+) -> VDemoPromptOutputs:
+    """
+    Prompts user with a message and waits for acknowledgment.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        message: The message to display in the prompt.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDemoPromptOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DEMO_PROMPT_METADATA)
+    params = v__demo_prompt_params(
+        message=message,
+    )
+    return v__demo_prompt_execute(params, execution)
+
+
+__all__ = [
+    "VDemoPromptOutputs",
+    "VDemoPromptParameters",
+    "V__DEMO_PROMPT_METADATA",
+    "v__demo_prompt",
+    "v__demo_prompt_params",
+]

niwrap_afni/afni/v__dice_metric.py

@@ -0,0 +1,315 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DICE_METRIC_METADATA = Metadata(
+    id="98eaa1a4d4837bef42b0135a72612d83719e6632.boutiques",
+    name="@DiceMetric",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDiceMetricParameters = typing.TypedDict('VDiceMetricParameters', {
+    "__STYX_TYPE__": typing.Literal["@DiceMetric"],
+    "base": InputPathType,
+    "dsets": list[InputPathType],
+    "max_roi": typing.NotRequired[float | None],
+    "forceoutput": typing.NotRequired[InputPathType | None],
+    "forceoutput_1": typing.NotRequired[InputPathType | None],
+    "echo": bool,
+    "save_match": bool,
+    "save_diff": bool,
+    "do_not_mask_by_base": bool,
+    "mask_by_base": bool,
+    "prefix": typing.NotRequired[str | None],
+    "ignore_bad": bool,
+    "keep_tmp": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@DiceMetric": v__dice_metric_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class VDiceMetricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__dice_metric(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__dice_metric_params(
+    base: InputPathType,
+    dsets: list[InputPathType],
+    max_roi: float | None = None,
+    forceoutput: InputPathType | None = None,
+    forceoutput_1: InputPathType | None = None,
+    echo: bool = False,
+    save_match: bool = False,
+    save_diff: bool = False,
+    do_not_mask_by_base: bool = False,
+    mask_by_base: bool = False,
+    prefix: str | None = None,
+    ignore_bad: bool = False,
+    keep_tmp: bool = False,
+) -> VDiceMetricParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base: Name of base (reference) segmentation.
+        dsets: Data sets for which the Dice Metric with BASE is computed. This\
+            should be the last option on the command line.
+        max_roi: The maximum possible ROI index. Default is 12 or based on\
+            LTFILE if specified.
+        forceoutput: If given, force output for each class in LTFILE.
+        forceoutput_1: If given, force output for each class in LTFILE.
+        echo: Set echo.
+        save_match: Save volume showing BASE*equals(BASE,DSET).
+        save_diff: Save volume showing BASE*(1-equals(BASE,DSET)).
+        do_not_mask_by_base: Do not mask dset by step(base) before computing\
+            Dice coefficient.
+        mask_by_base: Mask dset by the step(base) before computing Dice\
+            coefficient.
+        prefix: Use PREFIX for the output table. Default is separate results\
+            for each dset to stdout.
+        ignore_bad: Warn if encountering bad scenarios, but do not create a\
+            zero entry.
+        keep_tmp: Keep temporary files for debugging. Note that you should\
+            delete temporary files before rerunning the script.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@DiceMetric",
+        "base": base,
+        "dsets": dsets,
+        "echo": echo,
+        "save_match": save_match,
+        "save_diff": save_diff,
+        "do_not_mask_by_base": do_not_mask_by_base,
+        "mask_by_base": mask_by_base,
+        "ignore_bad": ignore_bad,
+        "keep_tmp": keep_tmp,
+    }
+    if max_roi is not None:
+        params["max_roi"] = max_roi
+    if forceoutput is not None:
+        params["forceoutput"] = forceoutput
+    if forceoutput_1 is not None:
+        params["forceoutput_1"] = forceoutput_1
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v__dice_metric_cargs(
+    params: VDiceMetricParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("@DiceMetric")
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base"))
+    ])
+    cargs.extend([
+        "-dsets",
+        *[execution.input_file(f) for f in params.get("dsets")]
+    ])
+    if params.get("max_roi") is not None:
+        cargs.extend([
+            "-max_N_roi",
+            str(params.get("max_roi"))
+        ])
+    if params.get("forceoutput") is not None:
+        cargs.extend([
+            "-forceoutput",
+            execution.input_file(params.get("forceoutput"))
+        ])
+    if params.get("forceoutput_1") is not None:
+        cargs.extend([
+            "-forceoutput",
+            execution.input_file(params.get("forceoutput_1"))
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("save_match"):
+        cargs.append("-save_match")
+    if params.get("save_diff"):
+        cargs.append("-save_diff")
+    if params.get("do_not_mask_by_base"):
+        cargs.append("-do_not_mask_by_base")
+    if params.get("mask_by_base"):
+        cargs.append("-mask_by_base")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("ignore_bad"):
+        cargs.append("-ignore_bad")
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    return cargs
+
+
+def v__dice_metric_outputs(
+    params: VDiceMetricParameters,
+    execution: Execution,
+) -> VDiceMetricOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = VDiceMetricOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__dice_metric_execute(
+    params: VDiceMetricParameters,
+    execution: Execution,
+) -> VDiceMetricOutputs:
+    """
+    Computes Dice Metric between BASE and each of the DSET volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDiceMetricOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__dice_metric_cargs(params, execution)
+    ret = v__dice_metric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__dice_metric(
+    base: InputPathType,
+    dsets: list[InputPathType],
+    max_roi: float | None = None,
+    forceoutput: InputPathType | None = None,
+    forceoutput_1: InputPathType | None = None,
+    echo: bool = False,
+    save_match: bool = False,
+    save_diff: bool = False,
+    do_not_mask_by_base: bool = False,
+    mask_by_base: bool = False,
+    prefix: str | None = None,
+    ignore_bad: bool = False,
+    keep_tmp: bool = False,
+    runner: Runner | None = None,
+) -> VDiceMetricOutputs:
+    """
+    Computes Dice Metric between BASE and each of the DSET volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base: Name of base (reference) segmentation.
+        dsets: Data sets for which the Dice Metric with BASE is computed. This\
+            should be the last option on the command line.
+        max_roi: The maximum possible ROI index. Default is 12 or based on\
+            LTFILE if specified.
+        forceoutput: If given, force output for each class in LTFILE.
+        forceoutput_1: If given, force output for each class in LTFILE.
+        echo: Set echo.
+        save_match: Save volume showing BASE*equals(BASE,DSET).
+        save_diff: Save volume showing BASE*(1-equals(BASE,DSET)).
+        do_not_mask_by_base: Do not mask dset by step(base) before computing\
+            Dice coefficient.
+        mask_by_base: Mask dset by the step(base) before computing Dice\
+            coefficient.
+        prefix: Use PREFIX for the output table. Default is separate results\
+            for each dset to stdout.
+        ignore_bad: Warn if encountering bad scenarios, but do not create a\
+            zero entry.
+        keep_tmp: Keep temporary files for debugging. Note that you should\
+            delete temporary files before rerunning the script.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDiceMetricOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DICE_METRIC_METADATA)
+    params = v__dice_metric_params(
+        base=base,
+        dsets=dsets,
+        max_roi=max_roi,
+        forceoutput=forceoutput,
+        forceoutput_1=forceoutput_1,
+        echo=echo,
+        save_match=save_match,
+        save_diff=save_diff,
+        do_not_mask_by_base=do_not_mask_by_base,
+        mask_by_base=mask_by_base,
+        prefix=prefix,
+        ignore_bad=ignore_bad,
+        keep_tmp=keep_tmp,
+    )
+    return v__dice_metric_execute(params, execution)
+
+
+__all__ = [
+    "VDiceMetricOutputs",
+    "VDiceMetricParameters",
+    "V__DICE_METRIC_METADATA",
+    "v__dice_metric",
+    "v__dice_metric_params",
+]